The self-assembly of DNA Holliday junctions studied with a minimal model

Thomas E Ouldridge, Iain G Johnston, Ard A Louis, Jonathan P K Doye

Research output: Contribution to journalArticlepeer-review

29 Citations (Scopus)


In this paper, we explore the feasibility of using coarse-grained models to simulate the self-assembly of DNA nanostructures. We introduce a simple model of DNA where each nucleotide is represented by two interaction sites corresponding to the sugar-phosphate backbone and the base. Using this model, we are able to simulate the self-assembly of both DNA duplexes and Holliday junctions from single-stranded DNA. We find that assembly is most successful in the temperature window below the melting temperatures of the target structure and above the melting temperature of misbonded aggregates. Furthermore, in the case of the Holliday junction, we show how a hierarchical assembly mechanism reduces the possibility of becoming trapped in misbonded configurations. The model is also able to reproduce the relative melting temperatures of different structures accurately and allows strand displacement to occur.

Original languageEnglish
Pages (from-to)065101
JournalJournal of Chemical Physics
Issue number6
Publication statusPublished - 14 Feb 2009


  • Base Sequence
  • DNA, Cruciform
  • DNA, Single-Stranded
  • Feasibility Studies
  • Kinetics
  • Models, Molecular
  • Monte Carlo Method
  • Nanostructures
  • Nucleic Acid Conformation
  • Nucleic Acid Hybridization
  • Temperature
  • Thermodynamics


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